The European champions dominated the error-prone Central Americans, often looked as if they could score at will but squandered a hatful of chances in an exciting but erratic display.
They were occasionally petulant and niggly and other World Cup referees may have sent off Villa late in the first half for slapping Emilio Izaguirre in the face as the players tangled at a corner.
The win took Spain second in Group H with three points, ahead of the Swiss on goal difference, and left them needing a win over Chile on Friday to guarantee qualification for the second stage.
It also gave them the first win by a European team over Latin American opposition in South Africa.
LIVE:Minute-by-minute coverage
"We created a lot of chances and could have won by more goals," said Spain coach Vicente del Bosque.
"But we were more vulnerable than we were against Switzerland."
"Honduras were quite adventurous, they came out and let us play."
Honduras coach Reinaldo Rueda, whose team have no points after two games, was realistic.
"The early goal tipped the balance of the game. There's not much to explain, we were playing a much superior team," said the Colombian.
Spain went quickly on the attack with Villa, who has an impressive 40 goals from 60 internationals, crashing an early effort against the crossbar.
Spain's 17th minute opener came after they snuffed out a rare Honduras attack.
Villa picked the ball up on the touchline, slipped between two defenders and then cut inside Osman Chavez to lift his shot past Honduras goalkeeper Noel Valladares.
Fernando Torres, included alongside Villa in attack, missed two golden chances in a minute just before the half hour as the Spanish continued to slice open the Honduran defence, which repeatedly gifted them possession.
Villa doubled Spain's lead six minutes into the second half when Jesus Navas cut the ball back to him on the edge of the area and his deflected shot looped over Valladares into the net.
Spain then won a penalty just after the hour when Navas fell theatrically in the area but Villa casually sent a low spot kick wide of the right-hand post.
The chances kept coming for Spain, Chavez clearing a Cesc Fabregas shot off the line after the substitute had rounded Valladares.
There were several breaks in which Spain's forwards outnumbered the Honduran defenders but they wanted one touch too many and allowed their opponents to regroup.
Follow FFT.com on Twitte
‘The pure simplicity of the way Slot has managed the squad is probably the biggest thing I could say about him. It’s not broken, so let’s get on with it’: Liverpool legend full of admiration for Jurgen Klopp's successor at Anfield
‘I trained at Spurs and thought they’d give me a chance. But I received a letter thanking me but saying they didn’t think I was good enough – I was gutted’: How Tottenham missed out on signing Wales legend John Toshack
